Transform cube face in the z up direction to vertice above (need automation method)
You may be asking for the DupliVerts feature.

In this case, the general steps would be:


Move the origin of the cube to the center of its top face;
First select the cube, then select the vertex cloud object, press CTRL P > Object;
Keep the parent object (vertex cloud) selected, go to Properties > Object Data > Duplication, select 'Verts". As shown in the image below.




P.S.: Remember to keep their origins staying at same location.